A 21-year-old Perth woman on her way home from a night out with friends was picked up in early hours of Sunday morning by a Swan Taxis driver who appeared to not be wearing pants.

Jessie Gravett booked a taxi using the Swan Taxis App about 12.30am from a North Perth house and was shocked to discover the driver was apparently not wearing pants.

Ms Gravett then captured photos of the man on her smart phone. He was also barefoot and his driver identification was allegedly hidden from view.

"There is possibly a legitimate reason for the lack of pants but if I would think he would stop driving and be a professional about it. Not pick girls up," she told WAtoday.com.au.

"I didn't take much notice of the driver when I got in, just shut the door and confirmed my drop off address in Spearwood, 35 minutes away.

"I immediately messaged my friends so they could keep tabs on me. I didn't want to draw attention to his lack of pants because I was unsure how he would react. I was very uncomfortable.

"I put my keys between my fingers and unzipped my sharp studded boots because I wasn't sure what his intentions were and I wanted to be prepared in case I needed to defend myself."

After arriving home safely she lodged a formally complaint and has submitted a statement to the Department of Transport.

"When I called they [Swan Taxis] said he had someone else in the car already for another job so at least they had track of him," she added.

When questioned about the incident by WAtoday.com.au Swan Taxis director Kevin Foley said the issue was now being investigated by the Department of Transport.

The driver has told his superiors he was wearing shorts.

According to the official taxi driver code of conduct distributed by the Department of Transport, a driver can be fined $200 for failing to wear regulation uniform, which must be "clean and in good repair" and must "wear the approved uniform in a neat and tidy manner".

The department has been in contact with Ms Gravett today and has said it would conduct an interview with the driver in question in the coming days.

"Based on the outcome of the investigation the driver may be subject to a License Suitability Conference, which will examine his suitability to hold a T extension [taxi licence]," the department told WAtoday.com.au via written statement this afternoon.

The statement also highlighted the importance of continuing installation of taxi camera surveillance units in cars, which the department feels will "simplify investigations and reduce the number of 'word against word' cases".

"It should be noted that taxi drivers are far more likely to be the victim of a crime, rather than a perpetrator, and as such the cameras are most likely to be used in identifying a crime against a taxi driver," the statement read.

The "pantless" allegations come a day after a psychiatrist at a Perth's women's health care centre advised women to re-think plans to take taxis home if they had been drinking alcohol.